…and this is a 
A phylogeny is a statement about the evolutionary history of organisms. Cladograms give branching order only, but phylograms include branch lengths as well. They inform us about diversification of lineages, patterns and rates of trait evolution, and the ages of taxa and timing of radiations.
The tree is a model for the history of life at the macroevolutionary level. Darwin fully embraced the idea.Trees now being built with DNA sequence data, using improved phylogenetic algorithms and increased computational power. We now have many well-supported phylogenies backed up by multiple lines of evidence.
There are issues with correlating gene trees with species trees — there can be discordance because of coalescence, etc.
There is some controversy about how much lateral gene transfer confounds the tree model of evolution. Are there parts where the tree model breaks down completely? Some microbiologists argue that archaeobacteria and prokaryote phylogeny can't be fit into a tree; the sensationalist New Scientist cover was shown. Ward thinks it is an exaggeration. Lateral gene transfer occurs, but Wu and Eisen analyzed 31 conserved protein coding genes in archaea and bacteria and a well-resolved phylogeny still emerges. This argues that lateral gene transfer was not so rampant that it obscures the central tree.
Ward showed a diagram from the Creation "Museum", illustrating their belief in an "orchard of life". They need to do a pseudo-phylogenetic analysis to show the "kinds" of life; much of their language has been taken from phylogenetic systematics. He calls it a cargo cult science.
What do the new molecular phylogenies tell us about evolution. Convergence is widespread; morphology can mislead us about evolutionary history. We're seeing well-supported clades emerging, such as the afrotheria, scattered within old morphological trees. We're also seeing a stronger biogeographic pattern in the data.
We also have tools for reconstructing ancestral states: we're using molecular/genetic data to infer and reconstruct an ancestral form. We can use this to reconstruct ancestral protein sequences, which can then be synthesized and their biological properties measured. Ward described the work of the Thornton lab on reconstructing glucocorticoid receptors.
Phylogenies also provide new insight into concepts of higher, more inclusive taxa. Specific example is the persistence of the dinosaur clade beyond the K/T boundary in the form of birds.
Non-pc taxon names: just as the fish taxon excludes tetrapods, inscts seem to be modified crustaceans, butterflies are modified moths, ants are modified wasps.
Life Science
Comments
Posted by: RagingBullwinkle
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October 30, 2009 5:45 PM
I just found out that lying fuck head Ray Comfort REMOVED three chapters from Origin of Species.
http://is.gd/4Iv97
It's really about time scientists get mad and start acting on it the way PZ does.
I remember Dawkins telling a crowd of us that it's a good thing he's giving away free copies, but I doubt he knew Comfort removed three chapters at that time.
Posted by: Sven DiMilo | October 30, 2009 5:48 PM
fixed
Huh? Crustaceans and hexapods are (probably) sister taxa, but are crustaceans paraphyletic without hexapods included? I don't think so. Same with the other two taxon pairs; my impression was that butterflies, moths, ants, and wasps are all perfectly good clades. No? Those examples are more like actinopterygians (ray-finned fishes) vs. sarcopterygians (lobe-finned fishes + tetrapods), rather than "fish" vs. "tetrapods." Unless I'm wrong.
Posted by: Pareidolius | October 30, 2009 6:01 PM
I am learning so much from all these posts (what I can comprehend without a science background, that is). But what I can't fully comprehend, I follow up on. I do miss the ranty bits though.
Posted by: TwoYaks | October 30, 2009 6:13 PM
Sven DiMilo beat me. A phylogeny is a hypothesis, not a statement. It hypothesizes about patterns of relatedness, and evolutionary distances among clades. And, like any good hypothesis, it should be subject to verification.
Posted by: Anonymous | October 30, 2009 6:20 PM
More like this. I don't even know if I quite understood the whole thing, but I certainly felt like I was learning
Posted by: TwoYaks | October 30, 2009 6:23 PM
I would also say that if we're finding more biogeographic for clades, it's only because we're much better at understanding the past patterns of terrain. We (at my department) do a lot of work on Beringial species, and it's only after the geologists had gone through and pained us a picture of the region that we can make sense of patterns in divergence. As an example, the deep clade of Blackfish on the North Slope of Alaska seems strange until one considers the Chukchi river in the Pleistocene didn't drain the right way to have connectivity with southern Beringia.
Posted by: lose_the_woo
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October 30, 2009 6:23 PM
Well, at least it's not just a Theory.
Posted by: Alex | October 30, 2009 6:31 PM
@2: No, even morphologists knew full well that butterflies emerged from moths and ants emerged from wasps. Traditional Linnean taxonomy reflects this as well: butterflies are but a few families within Lepidoptera, as ants are a family within Hymenoptera. It's the common names that reflect paraphyly.
Posted by: Nerd of Redhead, OM
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October 30, 2009 6:50 PM
That includes you, and it will until you accept your banning from this blog. You have nothing of interest for us, as you are a confirmed liar and bullshitter. So Bye-Bye Banned One.Posted by: ShaunOTD | October 30, 2009 7:19 PM
@Raging Bulwinkle #1
To be fair to the lying fuckhead, he admitted this up front, when he announced his intention to distribute the special edition.
I can't put my finger on the post, but I recall at the time speculating that he chose to omit chapters 11-13 because they deal more with the evidence than the theory.
Posted by: Gary Radice | October 30, 2009 7:32 PM
Just wanted to say mille grazie for the effort to live blog. You seem to be a good listener and the talks sound great. High signal/noise ratio, this.
Posted by: rb | October 30, 2009 7:36 PM
A phylogeny is an hypothesis about the relationships of homologies, the by product is a relationship of organisms.
Posted by: Sanity Jane
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October 30, 2009 7:38 PM
*snork*Winston Wolfe, Master Projectionist: You insult parrots by comparing them to puffed-up intellectually stunted blowhards such as yourself.
Posted by: rb | October 30, 2009 7:39 PM
sven,
yes, crustacea are very likely paraphyletic if you exclude insects.
Posted by: 'Tis Himself, OM
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October 30, 2009 7:41 PM
This describes my feelings as well.
Posted by: SEF | October 30, 2009 8:04 PM
Life is a cauliflower. While everyone else is concerned with how much interconnection between florets is caused by the melted cheese, the creationists are busy stripping the florets off the whole cauliflower on their plate, at various levels, and are arbitrarily declaring each one to be a separate entity. They need to learn how to cook and eat their education properly.
Posted by: Sven DIMilo | October 30, 2009 8:08 PM
I stand multiply corrected; thanks!
Posted by: Wowbagger | October 30, 2009 8:18 PM
The
saddesthappiest day of my life was when I had enough experience and enough knowledge and enough facts to come to the conclusion that, for the most part,mostall of the religious people in the world are full of shit.Fixed it for you.
Posted by: kopd | October 30, 2009 8:21 PM
"question authority"
That's when I left church behind.
"question everything"
That's when I left theism behind.
Neither had answers, only baseless assertions and unjustified demands. I'm much happier now.
Posted by: David Marjanović, OM | October 30, 2009 8:24 PM
Some people do use these terms this way, but actually, that's silly. It makes much more sense to use "cladogram" for the outcome of a phylogenetic ( = cladistic) analysis. Branch lengths are part of that; if you want to ignore them and just talk about the branching pattern, say you're talking about the topology of the cladogram – as people do all the time.
I'd rather start outright by saying "phylogenetic hypothesis" instead of "phylogeny". The phylogeny is a part of reality, and phylogenetic hypotheses are intended to (at least) approximate it.
Several analyses have found such a topology. I don't know by heart how well supported that is, but it's a fairly commonly published result.
It would, of course, nicely explain the complete lack of insects in the Cambrian to late Silurian or something, and it would explain the complete lack of marine insects throughout time.
And even that differs between languages. No further away from English than German, we find the word Schmetterling, which has a very similar origin as butterfly (it's from Czech smetana "cream"), and which is always translated as "butterfly", but that's wrong – if you're a zoologist, it means "lepidopteran", and if you're not, it means "lepidopteran that is big enough to be recognized as such by the naked eye". A better translation for "butterfly" is Tagfalter, a somewhat artificial term for the diurnal lepidopterans. I've seen classifications of Lepidoptera explained in terms of Großschmetterlinge, the clade of big ones, and Kleinschmetterlinge, the paraphyletic assemblage formed by the small ones.
We furthermore find the word Motte. It's almost obviously related to moth, but it refers exclusively to those tiny ones that eat stored food or clothes, never to, say, hawkmoths (Old World hummingbird analogues), which all count as Schmetterlinge, more precisely as Nachtfalter (the paraphyletic nocturnal part of Großschmetterlinge).
So, in German, "moths" are "butterflies" rather than the other way around. (Scare quotes here, not linguistic ones that indicate meaning.)
On to the post itself...
AFAIK without exception, these are cases where either no phylogenetic analyses had been done on morphological data before the first molecular ones came along, or where only much too small morphological analyses had been done.
After all, a phylogenetic analysis of Placentalia using several genes and a seriously large taxon sample (including enough fossils, which means shitloads of them) is a matter of a few months. A comparable analysis using morphological data is an entire PhD thesis or three.
The first morphological analysis of Placentalia that has a fairly serious taxon sample was presented at a conference last year and still hasn't been published. There have been, like, half a dozen serious molecular analyses of that clade since 2001.
The published morphological analyses of Placentalia are getting closer and closer to the molecular tree. They're not there yet, but I think in 5 or 10 years they will be.
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Winston Wolfe: I never believed everything my teachers told me; I'm surprised anyone does. So I can't believe everything you tell me. Put some evidence on the table, or take your grandiose claims back.
Posted by: Sven DiMilo | October 30, 2009 9:09 PM
Here's a recent article advocating a paraphyletic "crustacea" with hexapods embedded...cool stuff. Here's a purty phylogeny pitchur illustrating the idea.
And I was just ignorant about butterflies. Still not sure about ants within "wasps," though.
Posted by: Sven DiMilo | October 30, 2009 9:14 PM
Ah, now I see, because it's ((ants + vespids) + parisitoids). Cool.
Posted by: Chris P | October 30, 2009 10:16 PM
Hey Guys
You want fun - I'm listening to Meyer completely talking over the head of the audience here in Castle Rock. We are having a lecture on DNA.
Goodness knows what they expect the audience to do with this information.
Oh - its complexity. The DNA "Enigma" - what is the origin of DNA - it's digital information.
Snore
Posted by: InfuriatedSciTeacher | October 30, 2009 10:27 PM
Was all set to make a comment about termites, and had completely forgotten the convergent evolution bit...
Sven> Yea, had to look at that myself... the paper I saw explained it as ants having reduced the winged form to the dispersal stage (diploids only).
Posted by: gman | October 30, 2009 11:02 PM
This conference is fabulous. I've been sitting in on the phil sessions (R Richards, Dennett, Kitcher, Eugenie Scott, etc.) I even had a chat with Lewontin between sessions. Dennett hammered Richards pretty hard for his comments that Darwin had seen natural selection as a teleological (and possibly beneficient) process, at least in the early days. Dennett thinks D fully apppreciated the "mindlessness" of natural selection.
We hit a Lebanese restaurant on the way back and our server noticed my name tag. She mentioned she had been at the conference that morning. We assumed she was a student but NO-O-O, she had free admission because she was a DIRECT DESCENDANT of ... Darwin. So we got a picture with her. Biggest celebrity we're likely to meet here.
Returned to the hotel room and the best film on the religion/evolution controversy ever made was playing. You guessed it, Planet of the Apes.
Pretty good day, all in all.
Posted by: Zetetic
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October 31, 2009 12:13 AM
Winston Wolfe @ #9
Somehow I'd bet that like every other cdesign proponentsist that claims that they used to believe/defend evolution, that you can neither accurately describe the theory or the evidence supporting it.
Yet the creationists (and many of the religious) assert that they do know without any credible supporting evidence, or even trying to look for any! Unlike science and evolutionary theory.
True...and apparently if they know less than you do, then they are called creationists and I.D. supporters.
I agree, in fact the system for that is called science. Please let us know when you want to actually start questioning everything.Posted by: Chris P | October 31, 2009 12:28 AM
I managed to get a couple of questions in to Meyer at the end of his spiel in Castle Rock.
I suggested that design is no good without manufacturing, how was the DNA manufactured?
Meyer - I don't know.
Why do you have to throw rocks at Dawkins and Darwin in your presentation when you are talking origin of life and not evolution?
Meyer - Rambling answer that somehow implied that I was bad for asking it.
With all the Jesus talk in the little groups afterward it is clear this conference is not for me. American snake oil at its best. Apparently tomorrow its Behe and some people who want to link atheism to Darwinism.
Ugghh - I think I can spend my Saturday doing something useful. All I could do was cringe.
Posted by: Bill | October 31, 2009 1:22 AM
Hi Dr. Myers,
Thanks for an enlightening recapitulation of your day.
Basic Biology torrent!
For those of us downstream in the trenches of biotech enterprise, your reporting is very much appreciated.
Regards,
Bill Hennessey, M.D.
Posted by: darvolution proponentsist | October 31, 2009 3:23 AM
Winston Wolfe @9
Ahh, the ol' "I'm [was] an atheist, but ...."
This sums up just about every post of yours I've read, Mr. Uber-Mensa-Copypasta.
I mean seriously, what would Pharangula be like if anyone around here had the audacity to question PZ on any one of his posts ? The calamity that would ensue if folks around here started to challenging each other on points of fact, opinion, or hypothesis ?
Oh .. Wait ... That's Exactly What It *Is* Like Around Here.
But seriously, be sure to stop in again and remind us skeptics how to be skeptical. I now know that I should question every word that comes out of your mouth.
Is that you GoodScienceForYou ?
The Mensa routine, amongst other things, sounds very familiar.
Posted by: darvolution proponentsist | October 31, 2009 3:35 AM
Crap, I misspelled Pharyngula. It's time for bed.
Posted by: Thomas R. Holtz, Jr. | October 31, 2009 9:49 AM
Sven @#22,
Formicidae (ants) being nested among wasps has been the standard hypothesis even before the development of cladistics. Bees, too. Basically, all hymenopterans are wasps unless they evolve into bees or ants.
Posted by: Sven DiMilo | October 31, 2009 10:54 AM
Thanks again. Obviously, I R not A entomologist.
So, to clarify, ants, insects, tetrapods, and butterflies are perfectly good clades. The non-P(hylogenetically) C(orrect) taxon names are the larger groups within which these derived clades are embedded, i.e. "wasps," "crustaceans," "fishes," and "moths."
Of these common terms, though, I think only Crustacea has enjoyed any formal status at all in my lifetime.
However, informal names for paraphyletic grades serve a useful purpose, in my view. Monkeys, algae (more polyphyletic, I guess), reptiles: I still use these terms all the time even though I know full well they are not monophyletic groups.
Posted by: abb3w
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October 31, 2009 11:26 AM
Lateral gene transfer just means that the tree of life has a lot of mistletoe on it.
Posted by: Andreas Johansson
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October 31, 2009 12:03 PM
Thomas Holtz wrote:
Gah. I've always assumed "wasp" corresponded directly to Swedish geting (approx. = non-ant vespoid), which is how it's invariably translated in English-Swedish lexica. A closer Swedish equivalent then would be stekel, meaning "hymenopteran", esp. one that's not an ant, bee, or geting.
Posted by: John Scanlon, FCD | November 1, 2009 12:33 AM
One of the first introductions I recall to logic and biological nomenclature is being required to parse the statement "All butterflies are Lepidoptera, not all Lepidoptera are butterflies". I'm not sure when the idea of other Lepidoptera ("moths") being a less-natural group was folded into that, but I'm pretty sure I was aged in single figures. That was the paradigm example for a lot of thinking about phylogeny and other stuff since then.
Posted by: Monado
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November 1, 2009 1:24 AM
Anonymous, if you like this grab a copy of Carl Zimmer's Evolution.